Seurat QC

knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

Data loading and demultiplexing

Velocyto counts are loaded

## reading loom file via hdf5r...

## reading loom file via hdf5r...

## reading loom file via hdf5r...

## reading loom file via hdf5r...

Vireo clusters

BD sample tag distributions

BD demuxing

## # A tibble: 100 x 4
## # Groups:   case_id, donor_id [25]
##    case_id donor_id run_id   deltasum
##    <chr>   <chr>    <chr>       <dbl>
##  1 IKP007S donor0   sc10x05a        0
##  2 IKP007S donor1   sc10x05a        0
##  3 IKP007S donor2   sc10x05a        0
##  4 IKP007S donor3   sc10x05a        0
##  5 IKP007S donor4   sc10x05a        0
##  6 OT108   donor0   sc10x05a        0
##  7 OT108   donor1   sc10x05a        0
##  8 OT108   donor2   sc10x05a        0
##  9 OT108   donor3   sc10x05a        0
## 10 OT108   donor4   sc10x05a        0
## # … with 90 more rows

quality control

Before filtering

## An object of class Seurat 
## 100542 features across 30216 samples within 3 assays 
## Active assay: RNA (33514 features)
##  2 other assays present: emat, nmat

After filtering

## An object of class Seurat 
## 100542 features across 16749 samples within 3 assays 
## Active assay: RNA (33514 features)
##  2 other assays present: emat, nmat

Data normalisation

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Cell cycle scoring

Data scaling and dimensionality reduction

Elbow plot

Cell cycle phase

## png 
##   2